Japanese cedar (JC, Cryptomeria japonica) pollen allergens are the primary cause of JC pollinosis, a widespread seasonal allergic disorder and a significant public health issue in Japan. Nevertheless, rare information on repressing the pollen allergens released from JC pollen is available. This study aims to validate the repression of allergen Cry j 1 (the dominant JC pollen allergen that triggers JC pollinosis) using todomatsu oil produced from Abies sachalinensis waste, through surface plasmon resonance (SPR) experiments, sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and blind docking simulation. The findings revealed that todomatsu oil reduces the antibody reactivity and content of allergen Cry j 1 by 85.96% and 42.12%, respectively. The docking modeling suggested that alkyl hydrophobic forces, pi–sigma bonding, and hydrogen bonding are the principal motivating forces for todomatsu oil components to dock with allergen Cry j 1. More than 50% of the amino-acid residues docked by each todomatsu oil component (except α-pinene) are hydrophobic. Furthermore, oil components, especially β-maaliene, exhibited potent repression of allergen Cry j 1. Consequently, todomatsu oil, due to its inexpensive, available, convenient, and ecologically beneficial nature, is a viable measure to repress allergen Cry j 1.